User: Laven9

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Laven90
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Posts by Laven9

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Comment: C: A small detail when use VEP
... I see your point! Thank you for your advice! ...
written 6 days ago by Laven90
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A small detail when use VEP
... It is a small question I met when running `vcf2maf (VEP)`: If you run `vcf2maf (VEP)`, there is a fasta file needed to be offered. And my question is: since I used hg38.fa for my previous work, which fasta file should I give? hg38.fa or Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz from `VEP ...
vep written 7 days ago by Laven90 • updated 7 days ago by WouterDeCoster40k
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Comment: C: How long will bam-readcount take to run human samples?
... And may be I'd better try more recent tools too. Luckily, I have just found a review for this area and I think it will help a lot. I used to try Mutect2, but may be because I only offer two bam files ( a tumor bam and a normal bam), the result I got seems not exclude those SNPs. And I now guess it w ...
written 8 days ago by Laven90
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Comment: C: How long will bam-readcount take to run human samples?
... Sorry for troubling again. But I indeed have met with an annoying problem. When I tried to run `fpfilter` by `Varscan`, I got results like: 171661 variants in input file 171466 had a bam-readcount result 47692 had reads1>=2 0 passed filters 171661 failed filters 195 faile ...
written 8 days ago by Laven90
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Comment: C: How long will bam-readcount take to run human samples?
... Sorry for reply so late. Thanks for your help! Wow! I think I need to use those tools more flexibly. It seems much faster if I just run with `bam-readcount` the positions I need in the file. Thanks again for your help. It do help a lot! ...
written 10 days ago by Laven90
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Comment: C: How long will bam-readcount take to run human samples?
... Actually, I am a little worried. The size I got with `bam-readcounts` is as large as 200,000,000 KB with an input of 8,000,000. I am not sure if it is normal. The code I use is quite simple, as: bam-readcount my.bam -f hg38.fa > my.metric.txt ...
written 22 days ago by Laven90
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Comment: C: How long will bam-readcount take to run human samples?
... Oh! Is it that? Then I'll try `GUN parallel`. Thanks a lot ! ...
written 22 days ago by Laven90
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Comment: C: How long will bam-readcount take to run human samples?
... I am not sure whether `bam-readcounts` is a single threaded application, but the time it cost is much longer than 2-3 days. And I am going to try `mosdepth` now. Thanks for your advice! ...
written 22 days ago by Laven90
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How long will bam-readcount take to run human samples?
... I am now trying to run bam-readcounts. The sample I use is from human. But it takes almost 2-3 days to run one bam file. Is it normal? The size of my file is 8,000,000 KB. I am a little worried the time it takes is too long. ...
bam-readcounts written 23 days ago by Laven90 • updated 22 days ago by ATpoint19k
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How to interpret the output of gatk?
... Recently I run Gatk-Mutect2 to call the somatic mutations in my data, but I get a lot more (too much and seems abnormal) mutations than I expected. I supposed that there should be some filter I need to do to filter out those germline mutations. But I am not quite sure what filters should I do. Is th ...
gatk vcf2maf mutect2 written 5 weeks ago by Laven90 • updated 4 weeks ago by zephyr_falcon70

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